With a strong poison spray aimed at a bunch of flying insects, it's easy to imagine several of them falling together at the same time. Because flies are small and dirty creatures, we do not much care if many die at once. However, when it comes to humans, we care very much. When a large number of people, such as soldiers, are killed at one time from enemy fire, we may apply this idiom. It is also used regarding a large number of people falling ill from a mass sickness in a short space of time. Strangely, despite the unsympathetic image of comparing humans with flies, this idiom is used as often regarding friendly forces or groups of people we care about, as it is used regarding foes.